Mass Spectrometry Shared Resource - Project Summary/Abstract The Mass Spectrometry Shared Resource is a specialized facility with the primary goal of protein identification, characterization and quantitation. CSHL has had a peptide sequencing and proteomics facility for over two decades, but the facility was extensively re-equipped in 2008 following the recommendations of the External Advisory Committee, and was housed within the Keck Structural Biology laboratory on the ground floor of the Beckman building. The Resource provides Cancer Center members with access to up-to-date mass spectrometry instrumentation and specialized technical expertise. Services used by the majority of Cancer Center members include protein and protein complex identification, characterization of protein post translational modifications, quantitative peptide MRM assays and quantitative whole-proteome screens using 2D LCMS with iTRAQ or SILAC. More specialized services have undertaken quantitative phosphoproteomic and cysteine proteomics screens, lipid and carbohydrate analyses, metabolomics profiling and specific MRM assays of drugs and other small molecule metabolites. The Shared Resource performs all the data analysis for the quantitative screens and has developed new tools for the merging of large datasets across multiple, independent experiments. All of these services are highly technical and labor intensive. Without the Mass Spectrometry Shared Resource it would be extremely difficult for individual investigators to have access to this type of instrumentation and analyses and these types of services, which are often critical to their research programs. Over the last funding period the Resource has updated HPLC equipment to allow for high-resolution ultra-high pressure liquid chromatography (UHPLC) and built a dedicated 64-processor cluster for database searching. In summary, the Shared Resource provides the user group with state-of-the-art instrumentation and advanced technical support to help accelerate cancer research at CSHL. Over the past five years, the Mass Spectrometry Shared Resource was utilized by 16 Cancer Center members (43% of members), accounting for a majority of its use. This Resource contributed to 29 publications by Cancer Center members over this time period.